Research workbench
Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2S RNA aptamer
Analyse Structural basis for promiscuous binding and activation of fluorogenic dyes by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DB8
- Type
- protein + RNA
- Length
- 496 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab-heavy chain; RNA (60-mer); Fab-light chain
- Ligands
- G4A
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab-heavy chain | protein | 224 | 8% helix, 50% strand | — |
| R | RNA (60-mer) | rna | 60 | — | — |
| L | Fab-light chain | protein | 212 | 6% helix, 52% strand | — |
Ligands and binding sites
- G4A · 2-[(Z)-(3-methyl-1,3-benzoxazol-2(3H)-ylidene)methyl]-3-(3-sulfopropyl)-1,3-benzothiazol-3-ium · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.71 | 0.77 | 60 | empty |
| 2 | 511 | 0.59 | 0.74 | 58 | empty |
| 3 | 230 | 0.54 | 0.77 | 35 | empty |
| 4 | 76 | 0.32 | 0.74 | 15 | empty |
| 5 | 63 | 0.24 | 0.72 | 11 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1920 Ų buried · 20 hydrogen bonds · protein-protein
- H–R · 746 Ų buried · 20 hydrogen bonds · protein-nucleic
- R–L · 182 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6DB8 · Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA… · the same entry in another collection · chain H against H, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 6DB8 · PDBe 6DB8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.